Good catch. I've fixed it in release (version 1.22.4). This no longer
happens in devel since we moved completely to GRanges. The actual error
though is a bug in the methods package, and I've submitted a patch here:
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15691.

Michael


On Mon, Feb 24, 2014 at 7:40 AM, Marcel Schilling [guest] <
guest@bioconductor.org> wrote:

>
> I went through the rtracklayer vignette and got the following error:
>
> > library('rtracklayer')
> > data(targets)
> > targetRanges <- IRanges(targets$start,targets$end)
> > targetTrack
> <-with(targets,GRangesForUCSCGenome("hg18",chrom,targetRanges,strand,name,target))
> > subTargetTrack <- targetTrack[1]
> > browseGenome(subTargetTrack)
> Error in as.vector(x, "character") :
>   cannot coerce type 'closure' to vector of type 'character'
> > traceback()
> 12: as.character.default(call[[1L]])
> 11: as.character(call[[1L]])
> 10: callGeneric()
> 9: .local(object, range, track, ...)
> 8: (function (object, range, track, ...)
>    standardGeneric("browserView"))(<S4 object of class "UCSCSession">,
>        <S4 object of class "CompressedIRangesList">)
> 7: (function (object, range, track, ...)
>    standardGeneric("browserView"))(<S4 object of class "UCSCSession">,
>        <S4 object of class "CompressedIRangesList">)
> 6: do.call(browserView, viewParams)
> 5: .local(object, ...)
> 4: browseGenome(as(object, "RangedData"), ...)
> 3: browseGenome(as(object, "RangedData"), ...)
> 2: browseGenome(subTargetTrack)
> 1: browseGenome(subTargetTrack)
>
> Interestingly, the following works as expected:
> > browseGenome(subTargetTrack,range=base::range(subTargetTrack))
>
> To me, this seems to be a bug, since the I copied the code from the
> vignette and it failed.
> Of course, I might just be missing something.
>
>  -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> LC_MONETARY=en_US.UTF-8
>  [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C
>            LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] rtracklayer_1.22.3   GenomicRanges_1.14.4 XVector_0.2.0
>  IRanges_1.20.6       BiocGenerics_0.8.0   vimcom_0.9-93
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.30.1 bitops_1.0-6      BSgenome_1.30.0   RCurl_1.95-4.1
>  Rsamtools_1.14.3  stats4_3.0.2      tools_3.0.2       XML_3.98-1.1
> [9] zlibbioc_1.8.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

	[[alternative HTML version deleted]]

